Its a hard choice between Ninja & Trojan, They're both extremely strong classes, personally I enjoy playing a Ninja more than a Trojan but thats just because they do more damage.
There are a few differences between typical Katana-Ninja builds & the Sword/Blade/Club Trojan build... Namely, you don't have SS/FB, but instead you have TFB which has a much smaller range, but is a much more powerful killing tool against Trojans/Waters/Warriors. Likewise, you sacrifice Reflect for Substitute and Herc for ToxicFog.
Trojans are by far the more complicated class as there is alot of 'customizability' with what you choose as your Reborns, As a Ninja you are generally stuck with Nin-Nin-Nin, or Cyclone/Reflect-Nin... Both of which are PvP Powerhouses... It really comes down to what your better at playing really, If a Ninja is strongest, but you can't play it, you're going to be hopeless aren't you.
IMHO try both classes to about Lv110-120 then decide. (non-reborn will give a feel for the class without adding too much complication with extra RB skills)
For a little clarification on my points above, I play Katana/Katana Nin-Nin-Nin.